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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Protein Data Bank Entry:

3jqb

2.400 Å

X-ray

2009-09-06

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Pteridine reductase, putative
ID:Q581W1_TRYB2
AC:Q581W1
Organism:Trypanosoma brucei brucei
Reign:Eukaryota
TaxID:185431
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
B100 %


Ligand binding site composition:

B-Factor:7.416
Number of residues:23
Including
Standard Amino Acids: 22
Non Standard Amino Acids: 1
Water Molecules: 0
Cofactors: NAP
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.9661029.375

% Hydrophobic% Polar
43.6156.39
According to VolSite

Ligand :
3jqb_2 Structure
HET Code: DX6
Formula: C14H14N4O
Molecular weight: 254.287 g/mol
DrugBank ID: -
Buried Surface Area:71.23 %
Polar Surface area: 83.27 Å2
Number of
H-Bond Acceptors: 3
H-Bond Donors: 3
Rings: 3
Aromatic rings: 2
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 3

Mass center Coordinates

XYZ
36.937214.142632.594


Binding mode :
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Binding mode
BioSolveIT Image generated by PoseView
Protein
Binding Site
Ligand
Interaction pattern
hydrophobic (CA)
aromatic (CZ)
hydrogen bond acceptor (O)
hydrogen bond acceptor/donor (OG)
hydrogen bond donor (N)
positively ionized (NZ)
negatively ionized (OD1)
metal (ZN)

Legend:

Represent the protein/ligand binding mode, centered on the ligand
Dashed lines represents hydrogen bonds and metal interactions
Green residue labels for amino acids with hydrophobic contacts (green lines) to the ligand

Image generated using PoseView by BioSolveIT
BioSolveIT


LigandProteinInteraction
AtomAtomResidueDistance
(Å)
Angle (°)Type
NAAOGSER- 952.95167.72H-Bond
(Ligand Donor)
CAJCE1PHE- 974.340Hydrophobic
DuArDuArPHE- 973.660Aromatic Face/Face
CADSGCYS- 1683.420Hydrophobic
NALOHTYR- 1742.71153.3H-Bond
(Ligand Donor)
CAGCD2LEU- 2093.580Hydrophobic
CAECEMET- 2133.580Hydrophobic
CACCZ2TRP- 2213.50Hydrophobic
CAIC4NNAP- 2694.050Hydrophobic
CAJC3NNAP- 2694.050Hydrophobic
NAMO2ANAP- 2692.61151.72H-Bond
(Ligand Donor)
NAAO2ANAP- 2692.98134.26H-Bond
(Ligand Donor)